Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate CCNA_01648 CCNA_01648 adenosylmethionine-8-amino-7-oxononanoate
Query= BRENDA::Q88RB9 (425 letters) >FitnessBrowser__Caulo:CCNA_01648 Length = 420 Score = 181 bits (459), Expect = 4e-50 Identities = 121/350 (34%), Positives = 185/350 (52%), Gaps = 26/350 (7%) Query: 25 PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84 P+ V + + +I +GREL+D G+ HP + A+++Q+ + H F LA+ Sbjct: 27 PLPVVATRGARLILEDGRELVDGLASWWTACHGYNHPHIAGALRKQIETMPHVMFGGLAH 86 Query: 85 EPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIA------RAATGRAGVIAFTGG 138 EP L +++ +L+PGD D +GS AVE A+K+A R GR +AF GG Sbjct: 87 EPAYRLAKRLARLLPGDLDH-VFFAESGSVAVEIAMKMALQYQINRGVGGRTRFLAFRGG 145 Query: 139 YHGRTMMTLGLTG-KVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDAE 197 YHG T+ T+ + + +S G+MP + L ++D +A A Sbjct: 146 YHGDTLATMTVCDPEEGMHSLFAGVMPAQVIADLPRDPASEAALDALLA---------AR 196 Query: 198 PRDIAAIILEP-VQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256 +IAA+++EP +QG GG LP P E+++ LR L D+HG+LLI DE+ TG GRTG+ FAM+ Sbjct: 197 GHEIAAMLVEPLIQGAGGMLPHPPEVLRTLRRLADKHGVLLIFDEIFTGFGRTGSLFAMQ 256 Query: 257 QMGVAPDLTTFAKSIAGG-FPLAGVCGKAEYMDAI------APGGLGGTYAGSPIACAAA 309 GV PD+ T +K++ GG PL+ + +A A G TY +P+ACAAA Sbjct: 257 AAGVEPDIVTLSKALTGGTLPLSAAVARRHVFEAFWSDDPAAALMHGPTYMANPLACAAA 316 Query: 310 LAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVE 359 A +++FE+ V L GL + ++ DVR LG++ VE Sbjct: 317 NASLDLFEDGAWARDVARVSAALAEGLEPCRAGEGVV-DVRTLGAIGVVE 365 Lambda K H 0.320 0.138 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 461 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 420 Length adjustment: 32 Effective length of query: 393 Effective length of database: 388 Effective search space: 152484 Effective search space used: 152484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory